Global analysis of gene expression inXenopushindlimbs during stage‐dependent complete and incomplete regeneration

Abstract

Xenopus laevis tadpoles are capable of limb regeneration after amputation, in a process that initially involves the formation of a blastema. However, Xenopus has full regenerative capacity only through premetamorphic stages. We have used the Affymetrix Xenopus laevis Genome Genechip microarray to perform a large-scale screen of gene expression in the regeneration-complete, stage 53 (st53), and regeneration-incomplete, stage 57 (st57), hindlimbs at 1 and 5 days postamputation. Through an exhaustive reannotation of the Genechip and a variety of comparative bioinformatic analyses, we have identified genes that are differentially expressed between the regeneration-complete and -incomplete stages, detected the transcriptional changes associated with the regenerating blastema, and compared these results with those of other regeneration researchers. We focus particular attention on striking transcriptional activity observed in genes associated with patterning, stress response, and inflammation. Overall, this work provides the most comprehensive views yet of a regenerating limb and different transcriptional compositions of regeneration-competent and deficient tissues.

Beyond early development: Xenopus as an emerging model for the study of regenerative mechanisms

“…Taking this example then, one could predict that either regeneration is entirely controlled by reactivation of developmental mechanisms, or that the triggers that drive the choice between regeneration and wound healing vary between different tissues. One of these genes, Xnlrr-1, was also identified by Grow et al in their limb screen, as differentially expressed in st. 53 limbs at 1 and 5 days after amputation (Grow et al, 2006). Grow et al also identified several other genes in common with the Tazaki list (Grow et al, 2006).…”

“…However, the approaches used were rather different. Grow et al (2006) compared the transcriptome of regeneration competent (st. 53) and incompetent (st. 57) limb after 1 or 5 days of regeneration. Pearl et al (2008) compared st. 52 regenerating limbs to those blocked by transgenic expression of the Bmp inhibitor Noggin, 3 days after amputation.…”

“…By comparing the hindlimb regeneration data from Pearl et al (2008) and Grow et al (2006), 21 genes (22 probesets) were identified that appear to be consistently preferentially expressed in regenerating limb buds at 1, 3, and 5 days after amputation. Several of these have annotations and are shown in Table 2, the rest are transcribed loci of unknown function.…”

“…(1) Up regulated in 1, 3 and 5 day st. 52 hindlimb blastemas, information from analysis of data from (Grow et al, 2006;Pearl et al, 2008). (2) Up regulated in tail regeneration (Tazaki et al, 2005) and limb regeneration (Pearl et al, 2008).…”

Looking proximally and distally: 100 years of limb regeneration and beyond

“…It is also the rationale behind the new global bioinformatic and systems biology approaches that integrate the molecular elements of large genomic and proteomic databases into functional networks and pathways from which hypotheses about mechanisms emerge (Nabel, 2009). For example, global genomic and proteomic data on blastema formation in regenerating anuran and urodele limbs has been generated by a number of laboratories Habermann et al, 2004;Putta et al, 2004;Grow et al, 2006;Pearl et al, 2008;Smith et al, 2009;Monaghan et al, 2009;Rao et al, 2009) and in one case transcription factor pathways have been subjected to a systems biology analysis (Jhamb et al, 2011).…”